[REVIEW]: DREiMac: Dimensionality Reduction with Eilenberg-MacLane Coordinates

[editorialbot]

Submitting author: @LuisScoccola (Luis Scoccola)
Repository: https://github.com/scikit-tda/DREiMac
Branch with paper.md (empty if default branch): paper
Version: 0.3.0
Editor: @fabian-s
Reviewers: @mtsch, @raphaelreinauer
Archive: 10.5281/zenodo.10136542

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/4b1a5a47e47c84b15f3881fd7ae67764"><img src="https://joss.theoj.org/papers/4b1a5a47e47c84b15f3881fd7ae67764/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/4b1a5a47e47c84b15f3881fd7ae67764/status.svg)](https://joss.theoj.org/papers/4b1a5a47e47c84b15f3881fd7ae67764)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@mtsch & @RaphaelLilt, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @fabian-s know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @raphaelreinauer

📝 Checklist for @mtsch

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.07 s (646.3 files/s, 107443.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          17            545           1046           2087
Jupyter Notebook                13              0           2178            393
Markdown                         4             84              0            195
YAML                             5             20              6            184
TeX                              1             12              0            173
reStructuredText                 4            153            152             87
-------------------------------------------------------------------------------
SUM:                            44            814           3382           3119
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1043

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/s00454-011-9344-x is OK
- 10.4230/LIPIcs.SoCG.2023.57 is OK
- 10.1007/s00454-017-9927-2 is OK
- 10.1088/0266-5611/27/12/124003 is OK
- 10.1007/s00200-015-0251-x is OK
- 10.4230/LIPIcs.SoCG.2023.56 is OK
- 10.3389/fncom.2021.616748 is OK
- 10.1038/s41586-021-04268-7 is OK
- 10.1162/neco_a_01150 is OK

MISSING DOIs

- 10.1093/gmo/9781561592630.article.07825 may be a valid DOI for title: Dionysus

INVALID DOIs

- None

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[fabian-s]

👋🏼 @LuisScoccola @mtsch @RaphaelLilt
this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#REVIEW_NUMBER so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@fabian-s) if you have any questions/concerns.

[fabian-s]

@LuisScoccola: plz ignore missing DOI suggestion above, that's a false positive.

[fabian-s]

@editorialbot remove @RaphaelLilt as reviewer

[editorialbot]

@RaphaelLilt removed from the reviewers list!

[fabian-s]

@editorialbot add @raphaelreinauer as reviewer

[editorialbot]

@raphaelreinauer added to the reviewers list!

[raphaelreinauer]

Review checklist for @raphaelreinauer

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/scikit-tda/DREiMac?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@LuisScoccola) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[mtsch]

Review checklist for @mtsch

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/scikit-tda/DREiMac?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@LuisScoccola) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[fabian-s]

@raphaelreinauer, @mtsch:
Please feel free to comment and ask questions on this thread re. the open items on your checklists to help @LuisScoccola resolve any issues you come across.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues (or pull requests, even) on the software repository. When doing so, please mention openjournals/joss-reviews#REVIEW_NUMBER so that a link is created to this thread (and I can keep an eye on what is happening).

Thank you!

[mtsch]

@fabian-s I've completed my review. The paper is well-written and covers everything without being too long, the documentation is detailed and full of examples, and the software works exactly as described. I think DREiMac will make a great entry in JOSS!

[fabian-s]

@raphaelreinauer -- your checklist remains unfilled, is this due to issues with the paper/software you have identified?
if so, please comment and ask questions on this thread re. the open items on your checklists to help @LuisScoccola resolve any issues you have come across.

If not, please check the items that are in order so we can proceed with the review process.

Note that the JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues (or pull requests, even) on the software repository. When doing so, please mention #5791 so that a link is created to this thread (and I can keep an eye on what is happening).

Thank you!

[fabian-s]

@editorialbot generate pdf

[fabian-s]

@editorialbot check references

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/s00454-011-9344-x is OK
- 10.4230/LIPIcs.SoCG.2023.57 is OK
- 10.1007/s00454-017-9927-2 is OK
- 10.1088/0266-5611/27/12/124003 is OK
- 10.1007/s00200-015-0251-x is OK
- 10.4230/LIPIcs.SoCG.2023.56 is OK
- 10.3389/fncom.2021.616748 is OK
- 10.1038/s41586-021-04268-7 is OK
- 10.1162/neco_a_01150 is OK
- 10.21105/joss.02614 is OK
- 10.1145/2833157.2833162 is OK
- 10.21105/joss.00925 is OK
- 10.1007/s41468-021-00071-5 is OK

MISSING DOIs

- 10.1093/gmo/9781561592630.article.07825 may be a valid DOI for title: Dionysus

INVALID DOIs

- None

[fabian-s]

@LuisScoccola: plz ignore missing DOI suggestion above, that's a false positive.

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[raphaelreinauer]

@fabian-s I have some clarifying questions for the authors. How could I ask them?

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[fabian-s]

@editorialbot set 10.5281/zenodo.10136542 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.10136542

[fabian-s]

@editorialbot recommend-accept

note: "missing DOI" for Dionysius above is a false positive

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/s00454-011-9344-x is OK
- 10.4230/LIPIcs.SoCG.2023.57 is OK
- 10.1007/s00454-017-9927-2 is OK
- 10.1088/0266-5611/27/12/124003 is OK
- 10.1007/s00200-015-0251-x is OK
- 10.4230/LIPIcs.SoCG.2023.56 is OK
- 10.3389/fncom.2021.616748 is OK
- 10.1038/s41586-021-04268-7 is OK
- 10.1162/neco_a_01150 is OK
- 10.21105/joss.02614 is OK
- 10.1145/2833157.2833162 is OK
- 10.21105/joss.00925 is OK
- 10.1007/s41468-021-00071-5 is OK

MISSING DOIs

- 10.1093/gmo/9781561592630.article.07825 may be a valid DOI for title: Dionysus

INVALID DOIs

- None

[fabian-s]

"missing DOI" for Dionysius above is a false positive

[editorialbot]

👋 @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4783, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

@LuisScoccola - I'm the track editor, and will continue the processing shortly

[danielskatz]

I've suggested some minor changes in scikit-tda/DREiMac#15 - please merge this, or let me know what you disagree with, then we can proceed to acceptance and publication

[LuisScoccola]

@danielskatz thank you! I have merged it.

[danielskatz]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/s00454-011-9344-x is OK
- 10.4230/LIPIcs.SoCG.2023.57 is OK
- 10.1007/s00454-017-9927-2 is OK
- 10.1088/0266-5611/27/12/124003 is OK
- 10.1007/s00200-015-0251-x is OK
- 10.4230/LIPIcs.SoCG.2023.56 is OK
- 10.3389/fncom.2021.616748 is OK
- 10.1038/s41586-021-04268-7 is OK
- 10.1162/neco_a_01150 is OK
- 10.21105/joss.02614 is OK
- 10.1145/2833157.2833162 is OK
- 10.21105/joss.00925 is OK
- 10.1007/s41468-021-00071-5 is OK

MISSING DOIs

- 10.1093/gmo/9781561592630.article.07825 may be a valid DOI for title: Dionysus

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4788, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

@editorialbot accept

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Perea
  given-names: Jose A.
  orcid: "https://orcid.org/0000-0002-6440-5096"
- family-names: Scoccola
  given-names: Luis
  orcid: "https://orcid.org/0000-0002-4862-722X"
- family-names: Tralie
  given-names: Christopher J.
  orcid: "https://orcid.org/0000-0003-4206-1963"
doi: 10.5281/zenodo.10136542
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Perea
    given-names: Jose A.
    orcid: "https://orcid.org/0000-0002-6440-5096"
  - family-names: Scoccola
    given-names: Luis
    orcid: "https://orcid.org/0000-0002-4862-722X"
  - family-names: Tralie
    given-names: Christopher J.
    orcid: "https://orcid.org/0000-0003-4206-1963"
  date-published: 2023-11-17
  doi: 10.21105/joss.05791
  issn: 2475-9066
  issue: 91
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5791
  title: "DREiMac: Dimensionality Reduction with Eilenberg-MacLane
    Coordinates"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05791"
  volume: 8
title: "DREiMac: Dimensionality Reduction with Eilenberg-MacLane
  Coordinates"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.05791 joss-papers#4789
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05791
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[danielskatz]

Congratulations to @LuisScoccola (Luis Scoccola) and co-authors on your publication!!

And thanks to @mtsch and @raphaelreinauer for reviewing, and to @fabian-s for editing!
JOSS depends on volunteers and couldn't be successful without you

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.05791/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05791/status.svg
   :target: https://doi.org/10.21105/joss.05791

This is how it will look in your documentation:

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[mtsch]

Congratulations of the acceptance of the paper!

[ctralie]

Congratulations of the acceptance of the paper!

Thank you so much! And thank you for your time!